[English] 日本語
Yorodumi
- PDB-8gxe: PTPN21 FERM PTP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gxe
TitlePTPN21 FERM PTP complex
Components(Tyrosine-protein phosphatase non-receptor type 21) x 2
KeywordsPROTEIN BINDING/ HYDROLASE / PTPN21 / FERM / phosphotase domain / PTP / PTPD1 / HYDROLASE / PROTEIN BINDING- HYDROLASE complex
Function / homology
Function and homology information


protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoskeleton / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. ...Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, L. / Zheng, Y.Y. / Zhou, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity.
Authors: Chen, L. / Qian, Z. / Zheng, Y. / Zhang, J. / Sun, J. / Zhou, C. / Xiao, H.
History
DepositionSep 19, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 21
B: Tyrosine-protein phosphatase non-receptor type 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4603
Polymers68,4252
Non-polymers351
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.313, 228.246, 117.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 21 / Protein-tyrosine phosphatase D1


Mass: 34406.172 Da / Num. of mol.: 1 / Fragment: PTPN21 PTP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN21, PTPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16825, protein-tyrosine-phosphatase
#2: Protein Tyrosine-protein phosphatase non-receptor type 21 / Protein-tyrosine phosphatase D1


Mass: 34018.484 Da / Num. of mol.: 1 / Fragment: PTPN21 FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN21, PTPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16825, protein-tyrosine-phosphatase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEGMME 2000, HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→47.84 Å / Num. obs: 37344 / % possible obs: 99.69 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2893 / Rpim(I) all: 0.08139 / Net I/σ(I): 8.89
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.583 / Num. unique obs: 2494 / CC1/2: 0.809 / Rpim(I) all: 0.4333

-
Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZL

2bzl


Resolution: 3→47.84 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1896 5.08 %
Rwork0.2174 35448 -
obs0.2197 37344 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.11 Å2 / Biso mean: 91.374 Å2 / Biso min: 20.74 Å2
Refinement stepCycle: final / Resolution: 3→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 1 16 4597
Biso mean--47.01 41.74 -
Num. residues----565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.070.34531330.34422494262799
3.08-3.160.33341260.30462574270099
3.16-3.250.38181410.296224942635100
3.25-3.360.32081430.264125182661100
3.36-3.480.30311120.268625312643100
3.48-3.620.27071760.240125162692100
3.62-3.780.27641360.219325232659100
3.78-3.980.25711150.210325822697100
3.98-4.230.22311490.185324922641100
4.23-4.550.23251130.176425872700100
4.55-5.010.23631450.174525162661100
5.01-5.740.22851200.196325562676100
5.74-7.220.34441380.235125502688100
7.22-47.840.20511490.18442515266499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.0142-0.85531.36955.0259-1.73614.69460.08810.62970.3936-0.4003-0.0904-0.8480.16981.18920.03980.3816-0.04890.07411.0838-0.00340.3492-1.3754-49.915818.5525
25.01211.2903-0.6645.7051-0.00635.86270.10960.55580.759-0.31080.03230.2031-0.1854-0.1589-0.15050.29930.0024-0.01510.41730.03720.3091-27.7057-41.794112.6397
35.71530.2243-1.00183.76740.58725.69870.0992-0.0042-0.1382-0.0762-0.02780.18360.1257-0.13540.00660.30080.02570.05090.3460.02090.2167-32.7748-57.62219.2095
44.98090.1404-1.19084.1832-0.3712.32810.08380.32010.0464-0.6483-0.1055-0.13860.15630.5962-0.03870.36050.05560.01020.65210.01230.195-13.5308-56.100414.4255
51.18490.33290.59385.23821.47063.25540.08950.7235-1.1056-0.3712-0.42691.03860.5704-0.04990.24590.73570.1284-0.20360.508-0.20360.9859-34.1202-81.702910.8446
61.0356-0.8374-0.42093.139-1.78412.940.3118-0.1248-1.1238-0.288-0.3156-0.68241.07731.3946-0.00051.20.3765-0.18281.187-0.17661.5557-14.5382-98.87569.019
72.5971-0.58180.74771.67160.143.3751-0.05530.3149-0.9122-1.3136-0.49041.39791.1383-0.99930.42161.55540.0102-0.49790.8058-0.38842.1648-46.9887-99.1333-1.3282
81.7161.324-0.13337.3659-0.26121.02030.22510.21350.349-1.0321-0.52681.7344-0.2209-0.53190.06341.360.3161-0.82010.7835-0.56521.9742-44.9532-87.0633-1.2767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 878 through 912 )A878 - 912
2X-RAY DIFFRACTION2chain 'A' and (resid 913 through 987 )A913 - 987
3X-RAY DIFFRACTION3chain 'A' and (resid 988 through 1073 )A988 - 1073
4X-RAY DIFFRACTION4chain 'A' and (resid 1074 through 1171 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 130 )B20 - 130
6X-RAY DIFFRACTION6chain 'B' and (resid 131 through 213 )B131 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 286 )B214 - 286
8X-RAY DIFFRACTION8chain 'B' and (resid 287 through 307 )B287 - 307

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more